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Persistent homology

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https://www.readbyqxmd.com/read/28441305/step-by-step-technique-for-segmental-reconstruction-of-reverse-hill-sachs-lesions-using-homologous-osteochondral-allograft
#1
Hassanin Alkaduhimi, Michel P J van den Bekerom, Derek F P van Deurzen
Posterior shoulder dislocations are accompanied by high forces and can result in an anteromedial humeral head impression fracture called a reverse Hill-Sachs lesion. This reverse Hill-Sachs lesion can result in serious complications including posttraumatic osteoarthritis, posterior dislocations, osteonecrosis, persistent joint stiffness, and loss of shoulder function. Treatment is challenging and depends on the amount of bone loss. Several techniques have been reported to describe the surgical treatment of lesions larger than 20%...
April 24, 2017: Techniques in Hand & Upper Extremity Surgery
https://www.readbyqxmd.com/read/28418852/structural-homologies-between-phenformin-lipitor-and-gleevec-aim-the-same-metabolic-oncotarget-in-leukemia-and-melanoma
#2
REVIEW
Gábor Somlyai, T Que Collins, Emmanuelle J Meuillet, Patel Hitendra, Dominic P D'Agostino, László G Boros
Phenformin's recently demonstrated efficacy in melanoma and Gleevec's demonstrated anti-proliferative action in chronic myeloid leukemia may lie within these drugs' significant pharmacokinetics, pharmacodynamics and structural homologies, which are reviewed herein. Gleevec's success in turning a fatal leukemia into a manageable chronic disease has been trumpeted in medical, economic, political and social circles because it is considered the first successful targeted therapy. Investments have been immense in omics analyses and while in some cases they greatly helped the management of patients, in others targeted therapies failed to achieve clinically stable recurrence-free disease course or to substantially extend survival...
March 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28415283/quantifying-disorder-in-colloidal-films-spin-coated-onto-patterned-substrates
#3
Raheema Aslam, Sergio Ardanza-Trevijano, Kristin M Poduska, Anand Yethiraj, Wenceslao González-Viñas
Polycrystals of thin colloidal deposits, with thickness controlled by spin-coating speed, exhibit axial symmetry with local 4-fold and 6-fold symmetric structures, termed orientationally correlated polycrystals (OCPs). While spin-coating is a very facile technique for producing large-area colloidal deposits, the axial symmetry prevents us from achieving true long-range order. To obtain true long-range order, we break this axial symmetry by introducing a patterned surface topography and thus eliminate the OCP character...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28411218/the-conjugative-relaxase-trwc-promotes-integration-of-foreign-dna-in-the-human-genome
#4
Coral González-Prieto, Richard Gabriel, Christoph Dehio, Manfred Schmidt, Matxalen Llosa
Bacterial conjugation is a mechanism of horizontal DNA transfer. The relaxase TrwC of the conjugative plasmid R388 cleaves one strand of the transferred DNA at the oriT, covalently attaches to it and leads the ssDNA into the recipient cell. In addition, TrwC catalyzes site-specific integration of the transferred DNA into its target sequence present in the genome of the recipient bacterium. Here, we report the analysis of the efficiency and specificity of the integrase activity of TrwC in human cells, using the Type IV Secretion System of the human pathogen Bartonella henselae to introduce relaxase-DNA complexes...
April 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28405385/cranial-arterial-patterns-of-the-alpaca-camelidae-vicugna-pacos
#5
Haley D O'Brien
Artiodactyl cranial arterial patterns deviate significantly from the standard mammalian pattern, most notably in the possession of a structure called the carotid rete (CR)-a subdural arterial meshwork that is housed within the cavernous venous sinus, replacing the internal carotid artery (ICA). This relationship between the CR and the cavernous sinus facilitates a suite of unique physiologies, including selective brain cooling. The CR has been studied in a number of artiodactyls; however, to my knowledge, only a single study to date documents a subset of the cranial arteries of New World camelids (llamas, alpacas, vicugñas and guanacoes)...
March 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28402879/fragment-based-nmr-study-of-the-conformational-dynamics-in-the-bhlh-transcription-factor-ascl1
#6
Lorenzo Baronti, Tomáš Hošek, Sergio Gil-Caballero, Hadas Raveh-Amit, Eduardo O Calçada, Isabel Ayala, András Dinnyés, Isabella C Felli, Roberta Pierattelli, Bernhard Brutscher
The Achaete-scute homolog 1 (Ascl1) protein regulates a large subset of genes that leads neuronal progenitor cells to distinctive differentiation pathways during human brain development. Although it is well known that Ascl1 binds DNA as a homo- or heterodimer via its basic helix-loop-helix (bHLH) motif, little is known about the conformational sampling properties of the DNA-free full-length protein, and in particular about the bHLH domain-flanking N- and C-terminal segments, which are predicted to be highly disordered in solution...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28394908/natural-non-homologous-recombination-led-to-the-emergence-of-a-duplicated-v3-ns5a-region-in-hcv-1b-strains-associated-with-hepatocellular-carcinoma
#7
Hélène Le Guillou-Guillemette, Adeline Pivert, Elise Bouthry, Cécile Henquell, Odile Petsaris, Alexandra Ducancelle, Pascal Veillon, Sophie Vallet, Sophie Alain, Vincent Thibault, Florence Abravanel, Arielle A Rosenberg, Elisabeth André-Garnier, Jean-Baptiste Bour, Yazid Baazia, Pascale Trimoulet, Patrice André, Catherine Gaudy-Graffin, Dominique Bettinger, Sylvie Larrat, Anne Signori-Schmuck, Hénia Saoudin, Bruno Pozzetto, Gisèle Lagathu, Sophie Minjolle-Cha, Françoise Stoll-Keller, Jean-Michel Pawlotsky, Jacques Izopet, Christopher Payan, Françoise Lunel-Fabiani, Christophe Lemaire
BACKGROUND: The emergence of new strains in RNA viruses is mainly due to mutations or intra and inter-genotype homologous recombination. Non-homologous recombinations may be deleterious and are rarely detected. In previous studies, we identified HCV-1b strains bearing two tandemly repeated V3 regions in the NS5A gene without ORF disruption. This polymorphism may be associated with an unfavorable course of liver disease and possibly involved in liver carcinogenesis. Here we aimed at characterizing the origin of these mutant strains and identifying the evolutionary mechanism on which the V3 duplication relies...
2017: PloS One
https://www.readbyqxmd.com/read/28390873/chikungunya-virus-nsp4-rna-dependent-rna-polymerase-core-domain-displays-detergent-sensitive-primer-extension-and-terminal-adenylyltransferase-activities
#8
Ming Wei Chen, Yaw Bia Tan, Jie Zheng, Yongqian Zhao, Bee Ting Lim, Tobias Cornvik, Julien Lescar, Lisa Fong Poh Ng, Dahai Luo
Chikungunya virus (CHIKV) is an important arboviral infectious agent in tropical and subtropical regions, often causing persistent and debilitating disease. The viral enzyme non-structural protein 4 (nsP4), as RNA-dependent RNA polymerase (RdRP), catalyzes the formation of negative-sense, genomic and subgenomic viral RNAs. Here we report a truncated nsP4 construct that is soluble, stable and purified recombinantly from Escherichia coli. Sequence analyses and homology modelling indicate that all necessary RdRP elements are included...
April 5, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28389029/characterization-of-short-and-medium-chain-chlorinated-paraffins-in-outdoor-indoor-pm10-pm2-5-pm1-0-in-beijing-china
#9
Huiting Huang, Lirong Gao, Dan Xia, Lin Qiao, Runhua Wang, Guijin Su, Wenbin Liu, Guorui Liu, Minghui Zheng
Persistent organic pollutants (POPs) were listed in the Stockholm Convention, because of their adverse health effects, persistence, bioaccumulation and ubiquitous presence in the environment. Short chain chlorinated paraffins (SCCPs), chlorinated derivatives of n-alkanes, have been listed as candidate POPs under Stockholm Convention. Inhalation uptake was an important exposure pathway for non-occupational adult human and the pollution of particle matter has caused great concern. There are some studies focused on POPs such as polychlorinated biphenyls, polychlorinated dibenzo-p-dioxins and dibenzofurans and polybrominated diphenyl ethers in different size particles...
April 4, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28369973/persistent-symptomatic-parvovirus-b19-infection-with-severe-thrombocytopenia-transmitted-by-red-blood-cell-transfusion-containing-low-parvovirus-b19-dna-levels
#10
Keiki Nagaharu, Yuka Sugimoto, Yuji Hoshi, Takanori Yamaguchi, Ryugo Ito, Keiji Matsubayashi, Keiki Kawakami, Kohshi Ohishi
BACKGROUND: Transfusion-mediated human parvovirus B19 (PVB19) infection is rare but often causes severe hematologic disorders. In Japan, routine blood donor screening for PVB19 antigen (detection sensitivity, 10(6.4) IU/mL) using a chemiluminescent enzyme immunoassay (CLEIA) was introduced in 2008. However, there is no consensus on the minimal infectious dose of PVB19 permissible for red blood cells (RBCs). CASE REPORT: A 64-year-old man, who had received hemodialysis for diabetic nephropathy for 5 years, underwent an RBC transfusion for anemia caused by hemorrhagic enterocolitis...
April 2, 2017: Transfusion
https://www.readbyqxmd.com/read/28351765/health-risks-posed-to-infants-in-rural-china-by-exposure-to-short-and-medium-chain-chlorinated-paraffins-in-breast-milk
#11
Dan Xia, Li-Rong Gao, Ming-Hui Zheng, Jing-Guang Li, Lei Zhang, Yong-Ning Wu, Lin Qiao, Qi-Chang Tian, Hui-Ting Huang, Wen-Bin Liu, Gui-Jin Su, Guo-Rui Liu
Chlorinated paraffins (CPs) are complex mixtures of synthetic chemicals found widely in environmental matrices. Short-chain CPs (SCCPs) are candidate persistent organic pollutants under the Stockholm Convention. There should be great concern about human exposure to SCCPs. Data on CP concentrations in human breast milk is scarce. This is the first study in which background SCCP and medium-chain CP (MCCP) body burdens in the general rural population of China have been estimated and health risks posed to nursing infants by CPs in breast milk assessed...
June 2017: Environment International
https://www.readbyqxmd.com/read/28348565/a-novel-heterozygous-mutation-in-the-stat1-sh2-domain-causes-chronic-mucocutaneous-candidiasis-atypically-diverse-infections-autoimmunity-and-impaired-cytokine-regulation
#12
Kornvalee Meesilpavikkai, Willem A Dik, Benjamin Schrijver, Nicole M A Nagtzaam, Angelique van Rijswijk, Gertjan J Driessen, Peter J van der Spek, P Martin van Hagen, Virgil A S H Dalm
Chronic mucocutaneous candidiasis (CMC) is a primary immunodeficiency characterized by persistent or recurrent skin and mucosal surface infections with Candida species. Different gene mutations leading to CMC have been identified. These include various heterozygous gain-of-function (GOF) mutations in signal transducer and activator of transcription 1 (STAT1) that are not only associated with infections but also with autoimmune manifestations. Recently, two STAT1 GOF mutations involving the Src homology 2 (SH2) domain have been reported, while so far, over 50 mutations have been described mainly in the coiled coil and the DNA-binding domains...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28348242/structures-of-closed-and-open-states-of-a-voltage-gated-sodium-channel
#13
Michael J Lenaeus, Tamer M Gamal El-Din, Christopher Ing, Karthik Ramanadane, Régis Pomès, Ning Zheng, William A Catterall
Bacterial voltage-gated sodium channels (BacNavs) serve as models of their vertebrate counterparts. BacNavs contain conserved voltage-sensing and pore-forming domains, but they are homotetramers of four identical subunits, rather than pseudotetramers of four homologous domains. Here, we present structures of two NaVAb mutants that capture tightly closed and open states at a resolution of 2.8-3.2 Å. Introduction of two humanizing mutations in the S6 segment (NaVAb/FY: T206F and V213Y) generates a persistently closed form of the activation gate in which the intracellular ends of the four S6 segments are drawn tightly together to block ion permeation completely...
April 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28341629/persistent-homology-and-the-branching-topologies-of-plants
#14
Mao Li, Keith Duncan, Christopher N Topp, Daniel H Chitwood
No abstract text is available yet for this article.
March 24, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28327793/insights-into-cytochrome-bc1-complex-binding-mode-of-antimalarial-2-hydroxy-1-4-naphthoquinones-through-molecular-modelling
#15
Ana Carolina Rennó Sodero, Bárbara Abrahim-Vieira, Pedro Henrique Monteiro Torres, Pedro Geraldo Pascutti, Célia Rs Garcia, Vitor Francisco Ferreira, David Rodrigues da Rocha, Sabrina Baptista Ferreira, Floriano Paes Silva
BACKGROUND: Malaria persists as a major public health problem. Atovaquone is a drug that inhibits the respiratory chain of Plasmodium falciparum, but with serious limitations like known resistance, low bioavailability and high plasma protein binding. OBJECTIVES: The aim of this work was to perform molecular modelling studies of 2-hydroxy-1,4-naphthoquinones analogues of atovaquone on the Qo site of P. falciparum cytochrome bc1 complex (Pfbc1) to suggest structural modifications that could improve their antimalarial activity...
April 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28325102/building-up-and-breaking-down-mechanisms-controlling-recombination-during-replication
#16
Dana Branzei, Barnabas Szakal
The complete and faithful duplication of the genome is an essential prerequisite for proliferating cells to maintain genome integrity. This objective is greatly challenged by DNA damage encountered during replication, which causes fork stalling and in certain cases, fork breakage. DNA damage tolerance (DDT) pathways mitigate the effects on fork stability induced by replication fork stalling by mediating damage-bypass and replication fork restart. These DDT mechanisms, largely relying on homologous recombination (HR) and specialized polymerases, can however contribute to genome rearrangements and mutagenesis...
March 22, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28319048/amino-acid-insensitive-mtorc1-regulation-enables-nutritional-stress-resilience-in-hematopoietic-stem-cells
#17
Demetrios Kalaitzidis, Dongjun Lee, Alejo Efeyan, Youmna Kfoury, Naema Nayyar, David B Sykes, Francois E Mercier, Ani Papazian, Ninib Baryawno, Gabriel D Victora, Donna Neuberg, David M Sabatini, David T Scadden
The mTOR pathway is a critical determinant of cell persistence and growth wherein mTOR complex 1 (mTORC1) mediates a balance between growth factor stimuli and nutrient availability. Amino acids or glucose facilitates mTORC1 activation by inducing RagA GTPase recruitment of mTORC1 to the lysosomal outer surface, enabling activation of mTOR by the Ras homolog Rheb. Thereby, RagA alters mTORC1-driven growth in times of nutrient abundance or scarcity. Here, we have evaluated differential nutrient-sensing dependence through RagA and mTORC1 in hematopoietic progenitors, which dynamically drive mature cell production, and hematopoietic stem cells (HSC), which provide a quiescent cellular reserve...
April 3, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28314191/robust-detection-and-segmentation-of-cell-nuclei-in-biomedical-images-based-on-a-computational-topology-framework
#18
Rodrigo Rojas-Moraleda, Wei Xiong, Niels Halama, Katja Breitkopf-Heinlein, Steven Dooley, Luis Salinas, Dieter W Heermann, Nektarios A Valous
The segmentation of cell nuclei is an important step towards the automated analysis of histological images. The presence of a large number of nuclei in whole-slide images necessitates methods that are computationally tractable in addition to being effective. In this work, a method is developed for the robust segmentation of cell nuclei in histological images based on the principles of persistent homology. More specifically, an abstract simplicial homology approach for image segmentation is established. Essentially, the approach deals with the persistence of disconnected sets in the image, thus identifying salient regions that express patterns of persistence...
March 6, 2017: Medical Image Analysis
https://www.readbyqxmd.com/read/28284606/use-of-signature-tagged-mutagenesis-to-identify-genes-associated-with-colonization-of-sheep-by-e-coli-o157-h7
#19
Nancy A Cornick, Josh Pitzer, Amy F Helgerson, Melissa L Madsen, Kathy T Kurth, Qianjun Xiao, F Chris Minion
Outbreaks of Escherichia coli O157:H7 in the United States due to contaminated foods are a public health issue and a continuing problem. The major reservoir for these organisms is the gastrointestinal tract of ruminants where they are a member of the resident microbiota. Several factors that contribute to the colonization of cattle have been identified, but a systematic screen of genes that might contribute to the colonization and persistence phenotype in mature ruminants has not been reported. Using a sheep model of persistence, signature tagged mutagenesis (STM) was used to screen 1326 mutants for a persistence-negative phenotype of E...
March 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28278024/functional-elucidation-of-hypothetical-proteins-for-their-indispensable-roles-towards-drug-designing-targets-from-helicobacter-pylori-strain-hpag1
#20
Gagandeep Singh, Vikram Singh
Helicobacter pylori is a flagellated and slow growing gram-negative bacterium that persistently infects about half of the entire world population. In present study, we examined the proteome of Helicobacter pylori strain HPAG1 for identification of key uncharacterized proteins towards their novel regulatory functions. The complete proteome of this strain consists of 1539 proteins, out of which 520 proteins are annotated as hypothetical. Based on the functional motifs in their primary sequences, we were able to classify 254 of these hypothetical proteins into 6 functional categories...
March 3, 2017: Journal of Biomolecular Structure & Dynamics
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